[R] setMethod for "["

[Martin Morgan]

Hi Musa --

Musa Parmaksiz wrote:
> Hi R-Help,
> 
> Please consider the following simple case: I have a class like
> 
> setClass("myClass",
>                representation(x="matrix", y="character"))
> 
> and I would like to use the method *"["* for a *myClass* objects (but
> changing the default *drop* argument from TRUE to FALSE):
> 
> setMethod("[","myClass",
> function(x,i,j,...,drop=FALSE)
> {
>     x <- x at x
>     callNextMethod()

I think you are hoping that x at x will be subsetted, and it appears that 
it is. But I think this is a bug. 'callNextMethod' without any arguments 
should be using the 'x' in the signature. This should result in an error 
like the one seen here

setMethod("[",
           signature=signature(x="myClass"),
           function(x, i, j, ..., drop=FALSE)
       {
           callNextMethod()
       })

 > test[1,]
Error in x[i = i, j = , ...] : object is not subsettable

Normally, to change the value of the variable 'seen' by the next method, 
one would expect to have to write something like


setMethod("[",
           signature=signature(x="myClass"),
           function(x, i, j, ..., drop=FALSE)
       {
           callNextMethod(x=x at x, i=i, j=j, ..., drop=drop)
       })

You can now see how this is a little more complicated -- if j is missing 
in the original function call, then it can't be used in an assignment in 
callNextMethod. You'd have to write something like

setMethod("[",
           signature=signature(x="myClass"),
           function(x, i, j, ..., drop=FALSE)
       {
           if (missing(i) && missing(j))
               callNextMethod(x=x at x,,, ..., drop=drop)
           else if (missing(j))
               callNextMethod(x=x at x, i=i, , ..., drop=drop)
           else if (missing(i))
               callNextMethod(x=x at x, , j=j, ..., drop=drop)
           else
                callNextMethod(x=x at x, i=i, j=j, ..., drop=drop)
       })

or, since this is really an implementation that dispatches on the 
'misssing'-ness of i, j, a series of methods like

setMethod("[",
           signature=signature(
               x="myClass",
               i="ANY',
               j="missing")
            function(x, i, j, ..., drop=FALSE)
       {
            callNextMethod(x at x, i=i, , ..., drop=drop)
       })

Notice too how it is necessary to specify the argument list in quite an 
odd way, with a ',' for the 'missing' variable(s). This is because "[" 
is a so-called 'Primitive' function, and primitive functions match by 
position rather than the usual matching by name:

 > matrix(1:20,5)[4,2]
[1] 9
 > matrix(1:20,5)[j=4,i=2]
[1] 9

!

I read somewhere that when faced with learning complicated systems, 
otherwise intelligent people will develop wildly inaccurate stories to 
explain why the system 'works'. The above is my story.

Martin


>     x<-as.myClass(x)
> }
> )
> 
> suppose that *as.myClass* method has been already defined. Actually, all I
> want is to pass all the arguments to *"["* method for *matrix*, except
> changing the default behaviour for *drop*.
> 
> When I execute:
>> test<-new("myClass",x=cbind(1:3,4:6),y="a")
>> test[1,] # works as expected
> [1] 1 4
> 
>> test[1,drop=TRUE] # does not work
> Error: argument "j" is missing, with no default
> Error in callNextMethod() : error in evaluating a 'primitive' next method
> 
> but with a matrix the two cases work:
>> m<-cbind(1:3,4:6)
>> m[1,]
> [1] 1 4
>> m[1,drop=TRUE]
> [1] 1
> 
> Can you please advise me a solution for this problem?
> Thank you in advance for the help.
> 
> Musa
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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